


The Program

by The_Winter_Writer



Series: Bingo Challenge [8]
Category: Marvel Cinematic Universe, The Avengers (Marvel) - All Media Types
Genre: Alien Abduction, Alien Breeding Program, Alien Culture, Alpha Thor, Alpha rut, Alpha/Beta/Omega Dynamics, Alpha/Omega, Alternate Universe, Alternate Universe - Canon Divergence, Angst and Smut, Barebacking, Bottom Tony Stark, Breeding, Dubious Consent, Gags, Implied Mpreg, Kidnapping, Knotting, M/M, Magic, Mating Cycles/In Heat, Non-Consensual Touching, Non-Consensual Voyeurism, Objectification, Omega Tony Stark, Post-Avengers (2012), Powerless Thor, Restraints, Size Difference, Thor (Marvel) is Not Stupid, Tony Stark Needs a Hug, Top Thor
Language: English
Status: Completed
Published: 2017-12-17
Updated: 2017-12-17
Packaged: 2019-02-15 22:37:15
Rating: Not Rated
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 1
Words: 3,737
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/13040922
Author URL: https://archiveofourown.org/users/The_Winter_Writer/pseuds/The_Winter_Writer
Summary: Tony had gotten himself into a lot of horrible situations over the years but this one took the cake. Of all the reasons for someone to kidnap him Tony had never imagined this.





	The Program

**Author's Note:**

> I'm not sure how this one is going to be received but I'm going to post it and hope for the best. Oh...the gag mentioned in this...I kind of imagined it like the one Loki has on at the end of Avengers for those curious.
> 
> My eighth bingo square in my quest for a W-shaped bingo is B3: Alien Breeding Program. I'm not sure if anyone will notice but I kind of loosely based these "alien breeders" on people breeding animals for a certain result (though I know very little about that practice hence "loosely based") and that's how they see their whole operation.

Tony’s head felt off, fuzzy and wrong, as he blinked and tried to focus despite the dull pain throbbing at the back of his head. The room was white, almost sterile in the clinical kind of way it was laid out. His eyes darted around the room, taking in detail or the very obvious lack of detail and trying to figure out where he was before his brain started to come back online.

He was strapped down on his stomach and completely naked.

Fear had his entire body seizing at the position and the feeling of tempered air brushing his naked skin. Tony immediately tugged at his restraints and found both legs strapped down, both arms secured and not a single inch was given to where he could move. A gag filled his mouth.

The sound of footsteps had his heart hammering and his body tensing almost violently. Whoever it was moved around the room. He could hear things being moved and a soft kind of breathing that was terrifying in its own way because usually a kidnapper spoke by this point.

Then he could see who, or rather what, it was in the room with him.

The creature, _an alien—not another alien_ , was purple and wicked looking at it examined him with a detached expression on its face. When it spoke Tony only heard screeches and clicks. A cold hand gripped his face and moved to touch the rest of his body, examining and feeling, as he tried jerking away and failed repeatedly.

He barely heard the door open again.

“The Terran Omega is of good breeding stock, fertile and after thorough healing it is healthy to breed with multiple compatible beings. It is a perfect match for our breeding program.”

Breeding program?

Tony’s heart stopped and then started pounding violently. This was beyond a nightmare scenario. He had been working in his workshop; he had been talking with Jarvis and examining readings from the Stark satellites in between repairs to his latest Iron Man armor.

Then it was dark. His memory seemed to blur and he’d woken up here.

The purple alien spoke in its strange language but the other being, the one Tony could understand, seemed to know what it was saying. It made the entire thing a million times worse because he needed to know what _both_ of them were saying.

“Terrans are only compatible with so many races.” The second one seemed to be agreeing. “I already have the first compatible specimen ready. A full rut is imminent and the breeder has already received a fertility injection.”

He shouted his protest into the gag and yanked at his restraints. Neither alien seemed to care and continued to speak as though he wasn’t there, as though he was nothing and Tony started trembling.

For the first time he wished he was in that cave in Afghanistan.

In that cave no one had known what he was, no one on Earth who was still alive had known he was an Omega, but these aliens did and somehow they’d managed to remove him from his Tower.

A sound drew his attention and Tony watched the purple alien move to his side. The sound of a beep had him startling but nothing like the feeling of the bench he was strapped to tilting downward.

Soon enough his face was close to the ground and his ass was still raised up high, exposed and waiting.

One of the aliens left and when they returned the heavy, thick and coiling scent of an Alpha nearing rut filled the room. 

“Do you have any idea who you have captured?” the voice boomed and Tony tried to turn to stare, to confirm the owner of the voice but his position prevented him from seeing at that angle. “I am Thor, son of Odin and Prince of Asgard. You will—”

There was a sound of pain and Tony closed his eyes. They were able to subdue _Thor_. Thor who was a literal god of untold power and who he had thought was on Asgard with his homicidal brother.

At least he knew the Alpha they were going to be breeding him with. It was a small, very small, consolation and from the sounds of it Thor wouldn’t be the only one _breeding_ him. He’d managed to go his whole life with only a handful of people knowing he was an Omega, hiding his nature viciously, and now he had nowhere to hide.

 _At least it’s Point Break_.

Warmth seemed to press up against him and a large, thick and heavy cock brushed his ass. Tony’s breathing hitched and caught in his throat as the sound of chains echoed in the room and Thor’s breathing hitched audibly.

“How dare you—”

Now Tony could feel Thor jerking and he managed to look back to see that the aliens had bound Thor behind him. There appeared to be runes of some kind on the chains curled around ankles attached to very bare legs.

This was happening.

It was happening and it didn’t look like either of them were getting free anytime soon.

“Alpha,” The one alien Tony could understand addressed Thor, “You will stay in the breeding room until you have successfully bred your chosen Omega partner and then you will be given time to rest before we move you on to the next compatible Omega in this facility.”

“I will not.”

The increasing scent of Thor’s rut and the reluctant arousal flooding the air said otherwise.

They were left alone and Tony shivered as air brushed against his sensitive skin. His senses were filled with Alpha, rut, arousal and Thor’s own unique scent he vaguely remembered from meeting Thor. It spun his head, warmed his body and Tony could feel his body rapidly producing slick that had started to leak out of his clenching hole.

It was embarrassing and his cheeks flushed.

Clearly both his instincts and body agreed that Thor was a desirable partner.

It really didn’t help that he’d spent a lot of time that he’d been in Thor’s presence checking the Thunder God out and _wondering_ what all of that power would feel like pinning him down. He’d had to really focus on not dwelling on those thoughts and Jarvis had needed to use the suit to give him an extra injection of his suppressant.

“I am sorry, Omega.” Thor’s voice was rough and Tony could hear the true apology in Thor’s voice. He knew Thor had nothing to do with this. It was these fucking aliens kidnapping people and treating them like breeding stock. “They have managed to bind my strength and power. I cannot free either of us.”

Tony closed his eyes and worked on controlling his breathing. Thor probably didn’t even recognize Tony’s scent considering the last time they had met he had been usually special products to hide his true orientation.

“I will hold out as long as I can.”

 _Fuck_.

He needed his gag out yesterday so he could at least talk to Thor. Tony made a few distressed noises, trying to draw Thor’s attention and then he turned his head as best he could to catch Thor’s eye.

It somehow worked.

“ _Tony Stark_?” Thor’s eyes were glowing Alpha red, his cheeks flushed with arousal and a collar rested around his throat that had the same brightly flashing runes the chains keeping him in place had.

As Tony stared the runes seemed to glow brighter when Thor’s scent turned even more distressed. He wondered if the glowing corresponded to Thor attempting to access his locked power.

“What have they done to you?” there was concern and horror in Thor’s voice. Tony wondered how they had managed to capture Thor of all beings. Then something seemed to click for Thor and Tony watched those Alpha red eyes widen. “You are an Omega?”

_Of course not, Point Break, I just smell like one! It’s a new cologne I’m trying out._

Tony managed an agitated snarl that was muffled by his gag. He forced everything he could into his face even as his own cock started to harden and more slick leaked from his hole as Thor’s scent only became more potent.

He was getting to the point where he actually wanted to beg Thor to fuck him. The need for it was thrumming inside his body, writhing underneath his skin and twisting viciously in his gut.

His suppressed attraction to Thor really, really wasn’t helping him right now.

“I don't understand.” A few seconds passed and the look on Thor’s face had Tony wanting to cringe. “Did you deceive us?” there was a note of hurt in his voice and Tony figured it probably originated from all of the times that Loki deceived Thor.

Tony made a noise of agreement and forced himself not to react beyond that even as he made sure to put something like an apology on his face.

The expression must have registered as apologetic to Thor because Thor’s expression softened and Tony kind of hated it. He didn’t feel guilty in the least about hiding his orientation but he couldn’t really explain _why_.

“Ah.” The sound of understanding had him turning his face away and cursing the gag. He wasn’t used to being silent like this and it was driving him insane along with Thor’s very arousing scent. “I forgot what Jane told me about dynamics in your Realm. On Asgard Omegas are treasured and, when they choose to be, fierce warriors. Your Realm is backwards.”

There was nothing to say to that besides the fact that Tony would have clearly rather been born on Asgard if that was the case.

Thor groaned and cursed, “I am sorry, my friend.” It didn’t take back the fact that Tony could feel the hard length of Thor against him and it was more than obvious how aroused Thor was at the moment. “They have triggered my rut.”

That was pretty fucking obvious by the scent but at least Thor’s presence was having a very calming effect. He wasn’t alone in this. He _knew_ Thor and they had a shot. His chances of escape were far better with Thor’s aid.

And, if the aliens succeeded in breeding him this time, at least he would be carrying Thor’s child instead of some strange creature or being these aliens chose.

Guilt turned Thor’s scent sour and Tony’s nose wrinkled, an unwanted whine of protest escaping him at the scent and he hated his instincts. They were screaming underneath the surface now that the aliens had apparently flushed every last chemical suppressing his dynamic completely out of his system and left him raw.

Exposed.

It made getting a hold on his instincts near impossible and frustrating as fuck.

_They’re going to think what I did to the Ten Rings was nothing when I escape. I’m going to burn these fuckers to the ground._

He made a noise to get Thor’s attention when it became more than obvious that Thor was struggling harder and harder against giving into his own instincts the further into his rut he started to get.

Tony knew enough about Alphas, though little about Asgardian Alphas, to know that such a strong rut was actually painful. It would be even worse in the presence of an unclaimed fertile Omega.

The second Tony managed to make eye contact with Thor he made a huge show of going completely pliant in his restraints and used his body to raise his hips up just enough in invitation to let the Thunder God know he was giving consent as best he could.

It would be better for both of them.

It wasn’t ideal, this kind of thing couldn’t be, but he could make the best of the situation and assuage Thor’s guilt. And he’d heard, even as he’d protected his secret, that sex with an Alpha was the height of pleasure.

At least he’d learn if that was true or not.

_Do my delusions know no bounds? I just need to keep my head, I need Thor to keep his and then, maybe, we can get the fuck out of here._

He would deal with the reality of becoming a parent later. When he was free. When they were both free.

“I can’t.”

Tony made the motion again.

“Stark… _Tony_.” Thor looked away, “I can scent your fertility. This will result in a child. Possibly two.”

Of course it would.

That’s what these fucking aliens wanted. They had called this whole thing a breeding program. What other thing could they want but to breed him with Thor? It was giving in but at least in a controlled way.

At least this way Tony could choose as best he could.

At least he liked Thor, knew Thor and had been physically attracted to the Alpha before this whole thing.

“You and our child shall be treasured.” Thor’s voice was impossibly rough and Tony could feel the thick, blunt head of Thor’s large cock pushing against his loosened hole. His body had slipped into his heat, triggered by Thor’s scent and startling Tony with its growing intensity, as his body had quickly adapted for breeding by an Alpha. “I’ll retrieve an apple for you myself. Our healers will see to your every need.”

Tony wasn’t sure what Thor meant by that as his body started to heat, pleasure and need coursing through his body, as Thor’s cock started to sink in.

His breathing caught in his throat and his body thrummed as inch by unnaturally thick inch started to push into him. Tony felt like he was being split in two and at the same time everything in him was screaming its approval at having an Alpha penetrating him for the first time.

_Well he is a fertility god. What did you expect?_

By the time Thor was fully buried inside of him Tony was a whining, whimpering and shaking mess in his restraints. He wondered how it was possible to be this full, this stretched, and not lose his mind.

When Thor started to move, fucking into him harshly, part of Tony was undeniably thankful that Thor’s strength had been locked away. He didn’t want to be fucked to death. It wasn’t the worst way to go but he had so many things he still wanted to accomplish and he couldn’t do that to Pepper. To Rhodey and Happy.

Chains clanked with each powerful snap of Thor’s hips and pleasure raced through Tony each time Thor buried himself balls deep. The only thing he could do, strapped down and gagged, was lie there taking it repeatedly and delighting in the rush of pleasure.

Heavy balls slapped against him and each time Thor nailed his prostate Tony howled into his gag, overwhelmed and on edge, as his heat kicked in and he lost himself to the desperate need to be knotted.

This was far better than the controlled heats he’d experienced with toys when he’d needed to take a break from his suppressants.

It was a relief when Thor’s knot started to catch and tug on his rim, teasing almost, until the Thunder God slammed deep and rutted up against him. The knot pushed past Tony’s rim and caught inside as it swelled to the point that Tony didn’t think he could take the size of it.

His orgasm slammed into him and Tony blacked out after releasing a sharp cry of pleasure.

He blinked his eyes open to the feeling of a knot caught inside of him, warmth flooding his insides and the pleasured growls of an Alpha who had successfully knotted. Tony could feel the way his inner muscles milked Thor’s knot desperately in their attempt to coax a swift and successful breeding to quell his heat.

The aliens returned to the room, touching and examining his prone form, causing Thor to release threatening snarls all the while still grinding his knot into Tony and idly stroking his trembling muscles.

“Good.” The one he understood breathed. “A first successful coupling. The offspring of this pair should show superior strength and intelligence. An optimal combination.”

Tony floated on pleasure, pheromones and hormones as they spoke before disappearing from the room. He wasn’t sure how long he was caught on Thor’s knot but the Alpha made no attempt to communicate, far too lost in his rut and Tony didn’t bother trying to communicate.

Slowly Thor’s knot shrunk and finally came loose but it was only seconds before Thor was fucking into Tony again in his quest for his next knot. The words from before were gone and replaced by those same pleasured growls.

Tony simply laid there and let himself enjoy the feeling of having an Alpha fucking him for the first time in his life. It was as pleasurable as he’d heard.

* * *

They were in the breeding room for the entirety of Thor’s rut, a rut far longer than a human Alpha’s rut, while the aliens came to check the breeding progress and to ensure that Tony remained in good health.

The last day of Thor’s rut found Tony completely fucked out, belly rounded from multiple knottings and muscles limp as he brokenly whined into his gag. His heat had already been sated, womb successfully bred, days ago and now he was simply waiting out Thor.

He couldn’t have moved if he wanted.

The aliens come in, sedated Thor and removed him while leaving Tony strapped down with his sloppy ass raised up. He shuddered at the feeling of slick and come leaking out, how his hole clenched around nothing, as he panted softly into his gag and imagined killing every last alien here.

“Levels indicate a successful breeding.” Came a voice Tony had come to hate, “Terrans and Asgardians appear to be a truly compatible pair. We already have several buyers interested once the offspring have aged enough to be sold. The Frost Giant should prove just as successful once this Omega births and is ready for another breeding.”

Tony protested into his gag, _Giant? I’m a human you fucking idiots I can’t take a fucking giant!_ , but they ignored him and continued talking about selling the child that Thor had put into his womb.

They were going to sell his kid over his cold, dead body. Fuck that. He might not have planned on having a kid but he sure as Hell wasn’t going to give it up.

“There is a huge market for half-Asgardians. It is fortunate we captured one for our program.”

They freed him from his restraints, removed him from the bench and easily carried him to an examination table where he was strapped down again. He cringed at the bright light shining in his eyes and flinched when they took samples, touching and prodding, while Tony laid there.

“No damage.”

Clicking and screeching came from the purple alien while it pressed against his tender muscles.

“The readings are indicating two offspring.” A sound of agreement, “They will make good additions to the breeding program. Producing two offspring during the first breeding is very promising. Hopefully the next coupling will prove just as fruitful.”

The second they freed him from the table Tony immediately tried struggling away, jerking and yanking, but they overpowered him and took him into the Spartan bathroom he’d been in during Thor’s rut.

It was humiliating being hosed down, scrubbed and cleaned, but there was nothing he could do while being completely powerless, exhausted and well fucked. They finished in the bathroom and hauled him down the hallway where Tony could see into rooms exactly like the one he’d just spent Thor’s rut in.

 _Breeding rooms_.

He could see others strapped down as he was and being bred by various aliens. Horror filled him at the sights and the lack of sound. He hadn’t realized the rooms were soundproof or that one whole wall to the room was made of clear glass for viewing.

Aliens had been able to see him caught on Thor’s knot and being bred without him even knowing. He felt completely violated. Somehow more violated then being strapped down and treated like an animal.

“Once breeder AES0529 gives birth and recovers there has been a request to have it bred by the Frost Giant brought in with the Asgardian. Tests indicated compatibility.”

Tony struggled and writhed as they carried him down another hallway that was designed the same way. The walls of the hallway were glass, except for where there were doors, that let those walking past see into the small rooms.

One side appeared to hold beings in various stages of pregnancy, runes glowing brightly on the walls, while the other side, Tony guessed, housed those who were being treated like studs.

The purple alien placed its hand on a pad and opened the door to an empty room. He was carried inside, injected and then dropped onto what Tony guessed was a bed. It was piled with blankets and pillows.

Tony watched as one of the aliens pressed its hand to the wall, near a set of runes, before chanting something in a language Tony would give his fortune to understand as light seemed to pulse and something heavy felt as though it had settled against his skin.

 _Fucking magic_.

Now the alien seemed fit to address him and Tony’s brain was trying to think through the fuzzy feeling that was slowly clouding his senses. “Do not be alarmed. The runes will ensure your gestation period is significantly shortened and your health is maintained. This helps to ensure that you can produce a significantly larger number of offspring then your kind typically produces.”

That sounded ominous.

Tony really fucking hated magic.

His eyes drooped as the drug they’d injected him with started to creep through his veins and his body slumped into the soft pillows. He barely registered the gag and his restraints being removed before the aliens were leaving the room.

The door shut, a beep sounded and Tony distantly knew it had locked. He blinked at the glass wall and stared across into the small room across from his.

Loki stared back at him. A collar similar to the one on Thor was wrapped around his neck and there wasn’t a sign of his impressive armor anywhere in the cell. It was the last thing he registered as he slipped into unconsciousness.

**Author's Note:**

> So...I wrote that. That's what I came up with for "Alien Breeding Program" and I did my best to steer it in such a manner that it was more dubcon than anything and I'm hoping I pulled that off. I kind of based it on breeders who breed certain animals for a specific result and then sell the offspring to interested owners/buyers. Also I wanted to point out that in this verse Tony WAS actually attracted to Thor prior to the whole kidnapping/breeding program thing (but it was a shitty situation) and that interest was returned by Thor (but since this is Tony's POV that didn't really fit).
> 
> I did leave it implying that the next individual to breed Tony would be Loki (and we're also ignoring the whole "cross breeding" thing because this is fanfic and also the Marvel universe/ABO universe).
> 
> Ugh I'm just a bit nervous about this one because it was so hard to find the right balance, to deal with the focus of the bingo square and to work with these two in this particular situation because I didn't want noncon between Thor and Tony. I really wanted ThunderIron which is why I chose them for this particular square (also why wouldn't aliens in an alien breeding program want Thor? Or Tony? It makes sense dammit).
> 
> I don't have immediate plans to continue this one (because I'm sure readers might wonder and I'm still focusing on my bingo challenge plus other ideas even if I do have stuff down for this one in a notes doc) but I'm not leaning towards having an unhappy ending to this particular verse if that helps anyone wondering after where I left off. I'm leaning away from an unhappy ending mostly because I don't like those (but there is angst as you would expect with this kind of setting and they really are in a bad spot).
> 
> Ummm...so...what did you all think? Was it at least an interesting read? Somewhat enjoyable?


End file.
